Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate Ac3H11_1341 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1341 Length = 442 Score = 392 bits (1007), Expect = e-113 Identities = 204/435 (46%), Positives = 279/435 (64%), Gaps = 20/435 (4%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F T +HAG + D +RA PI+ TTS+VF+N++H S LF L+ G VYSR NPT Sbjct: 15 FGTRAIHAGAQP--DPVTGARATPIHQTTSFVFDNAEHASSLFNLQTFGNVYSRISNPTV 72 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 V EERIA+LE G AALA +SG AAQ A+ + TGD+IV+ S LYGGT Q + F R Sbjct: 73 AVFEERIASLENGRAALACASGMAAQMAALLAILKTGDHIVAASTLYGGTVGQLGVGFAR 132 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 GIE FV+ +PE F + T+AVY ETIGNP NV D + +AH HG+P+++DN Sbjct: 133 LGIETTFVDPADPENFARAMRPNTRAVYGETIGNPLVNVLDIAAVAEVAHAHGVPLIIDN 192 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T A Y C P+ GADIV HSATK+IGGHGTT+GG++V+ G+FPW + KFP+ +P+ Sbjct: 193 TV-ASPYLCNPLALGADIVVHSATKYIGGHGTTMGGVVVEGGQFPWDN--GKFPEMVEPS 249 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 YHG + E +G+ Y + R E+ R G +++P ++ LLQG ETL LR H NAL Sbjct: 250 RAYHGVKFYETFGDFGYTMKARMEVNRTFGGVLSPMNAWQLLQGAETLHLRMREHCRNAL 309 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYL-----SNGFGGVLSFGVKDLPNADKET 359 +AK+L+ P V+WV+YPGL+ + + A+K + G G+L+FGVK A Sbjct: 310 AVAKFLQSHPQVAWVNYPGLSDSPYFDLAQKQFRAVDGAPGASGILTFGVKGGATA---- 365 Query: 360 DPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSV 419 G + +D + S+LAN+GDAKTLVI P TTH+QLN++E +GV+ D++R+SV Sbjct: 366 ------GEKFIDACEFLSHLANIGDAKTLVIHPASTTHRQLNEEELARAGVSADMVRLSV 419 Query: 420 GIEFIDDIIADFQQS 434 GIE +DDI+ D Q+ Sbjct: 420 GIEDLDDILWDIDQA 434 Lambda K H 0.317 0.136 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 588 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 442 Length adjustment: 32 Effective length of query: 412 Effective length of database: 410 Effective search space: 168920 Effective search space used: 168920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory